magic_assay_names {MAST}R Documentation

Default assay returned

Description

Methods in this package operate on log-transformed (multiplicative scale) expression. We attempt to check for this at construction, and then over-ride the assay method to return the "layer" containing such log-transformed data.

Usage

magic_assay_names()

## S4 method for signature 'SingleCellAssay,missing'
assay(x, i, ...)

Arguments

x

SingleCellAssay

i

must be missing for this method to apply

...

passed to parent method

Details

By default we return the assay whose names, as given by assayNames(x), matches the first element in the vector c('thresh', 'et', 'Et', 'lCount', 'logTPM', 'logCounts', 'logcounts').

Functions

Examples

data(vbetaFA)
assay(vbetaFA)[1:3,1:3]
assay(vbetaFA, 'thresh') = assay(vbetaFA)*0 - 9 
assay(vbetaFA)[1:3, 1:3]

[Package MAST version 1.8.2 Index]